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| Status |
Public on Dec 01, 2013 |
| Title |
NS_D15 |
| Sample type |
SRA |
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| Source name |
Non-stress control_15 min
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| Organism |
Clostridium acetobutylicum |
| Characteristics |
stressed with: none (no-stress control)
time point: 15 min
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| Growth protocol |
Cultures of C. acetobutylicum were grown in batch mode in 4-L bioreactors up to the mid-exponential phase of growth (O.D ~ 1.0), at which point the cultures were stressed with three different concentrations of butanol and butyric acid, respectively, in 3 biological-replicate experiments each. For butanol stress experiments, the cultures were stressed with 30 mM (low), 60 mM (medium) and 90 mM (high), while for butyric-acid stress, 30 mM (low), 40 mM (medium) and 50 mM (high) butyrate concentrations were used. Cultures were sampled at 15, 30, 60 and 75 min post stress for RNA isolation and sequencing.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples for RNA isolation were collected by centrifugation at 5000 rpm at 4°C for 10 min and the pellets were stored at -80°C. RNA isolation was carried out using the Qiagen’s miRNeasy Mini kit (Jones et al, 2008). After RNA extraction, mRNA and sRNA were enriched by using Microbe Express kit from Ambion ® kit as per the manufacturer’s protocol.
The Ovation Prokaryotic RNA-Seq System (NuGEN® Technologies, Inc, San Carlos, CA) was used to synthesize cDNA from 500 ng of enriched RNA. 50 μL of cDNA was used to construct libraries using the TruSeq DNA Sample preparation kit .
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The adapter sequences were trimmed from raw sequence reads.
Remaining small RNA sequences were chopped to a maximum length of 50 nucleotides.
Reads shorter than 18 nucleotides were discarded.
Reads were aligned to Clostridium genome using Tophat v2.0.5, allowing 0 mismatches
Genome_build: Clostridium acetobutylicum (http://www.ncbi.nlm.nih.gov/genome/1022?project_id=57677)
Supplementary_files_format_and_content: tag count file
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| Submission date |
Jun 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
[email protected]
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| Phone |
314-587-1422
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| Organization name |
Donald Danforth Plant Science Center
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| Lab |
Meyers lab
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| Street address |
975 N Warson Road
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
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| Platform ID |
GPL17364 |
| Series (1) |
| GSE48349 |
Transcriptional profile (mRNA and sRNA) of Clostridium acetobutylicum to metabolite stress, butanol and butyrate |
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| Relations |
| BioSample |
SAMN02214367 |
| SRA |
SRX316202 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1176114_NS_D15.txt.gz |
42.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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